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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-08, 15:02 based on data in: /home/chengxin/pmultiqctest/test_lfq/results


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 6/6 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        BSA1_F1.mzML111111
        BSA1_F2.mzML121111
        BSA2_F1.mzML211222
        BSA2_F2.mzML221222
        BSA3_F1.mzML311333
        BSA3_F2.mzML321333

        HeatMap

        This plot shows the pipeline performance overview

        This plot shows the pipeline performance overview. Some metrics are calculated.

        • Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
        • Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
        • Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
        • Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
        • Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
        • Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
        • Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
        • Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
        loading..

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 5/5 columns.
        Total MS/MS SpectralTotal MS/MS Spectral IdentifiedIdentified MS/MS Spectral CoverageTotal Peptide IdentifiedTotal Protein IdentifiedTotal Protein Quantified
        3136
        199
        6.35%
        55
        44
        39

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 6/6 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        BSA1_F1.mzML
        1
        1
        1
        26
        24
        11
        10
        BSA1_F2.mzML
        1
        1
        2
        16
        15
        6
        5
        BSA2_F1.mzML
        2
        2
        1
        26
        24
        12
        10
        BSA2_F2.mzML
        2
        2
        2
        16
        16
        6
        5
        BSA3_F1.mzML
        3
        3
        1
        17
        16
        9
        5
        BSA3_F2.mzML
        3
        3
        2
        9
        9
        3
        4

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Spectra Tracking

        This plot shows the quantms pipeline mzML tracking

        This table shows the changes in the number of spectra corresponding to each input file during the pipeline operation. And the number of peptides finally identified is obtained from the PSM table in the mzTab file. You can also remove the decoy with the remove_decoy parameter.:

        • MS1_Num: The number of MS1 spectra extracted from mzMLs
        • MS2_Num: The number of MS2 spectra extracted from mzMLs
        • MSGF: The Number of spectra identified by MSGF search engine
        • Comet: The Number of spectra identified by Comet search engine
        • Final result of spectra: extracted from PSM table in mzTab file
        • Final result of Peptides: extracted from PSM table in mzTab file
        Showing 6/6 rows and 5/5 columns.
        Spectra FileMS1_NumMS2_NumFinal result of spectraMSGFFinal result of Peptides
        BSA1_F1.mzML
        286
        481
        59
        207
        25
        BSA1_F2.mzML
        278
        639
        35
        295
        16
        BSA2_F1.mzML
        257
        557
        34
        219
        26
        BSA2_F2.mzML
        267
        609
        31
        250
        16
        BSA3_F1.mzML
        290
        383
        25
        157
        16
        BSA3_F2.mzML
        298
        467
        15
        196
        9

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Oversampling Distribution

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.

        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.

                    * Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
        
        loading..

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        Showing 50/50 rows and 10/10 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage Intensity123123
        1
        P02769|ALBU_BOVIN
        AEFVEVTK
        0.857
        97756193.333
        154659700.000
        88615720.000
        49993160.000
        2
        tr|A9FP67|A9FP67_SORC5
        AFNRMYR
        0.167
        355427.600
        355427.600
        nan
        nan
        3
        P62739|ACTA_BOVIN
        AGFAGDDAPR
        0.500
        97508.140
        97508.140
        nan
        nan
        4
        P02769|ALBU_BOVIN
        AWSVAR
        0.857
        11545579.500
        14145840.000
        8945319.000
        nan
        5
        P02769|ALBU_BOVIN
        C(Carbamidomethyl)C(Carbamidomethyl)TESLVNR
        0.857
        11820299.300
        20567660.000
        11201284.900
        3691953.000
        6
        sp|O46375|TTHY_BOVIN
        C(Carbamidomethyl)PLM(Oxidation)VK
        0.857
        245169.950
        295550.000
        194789.900
        nan
        7
        sp|O46375|TTHY_BOVIN
        C(Carbamidomethyl)PLMVK
        0.857
        474947.600
        474947.600
        nan
        nan
        8
        P02769|ALBU_BOVIN
        DDPHAC(Carbamidomethyl)YSTVFDK
        0.857
        3881159.000
        1764358.000
        nan
        5997960.000
        9
        P02769|ALBU_BOVIN
        DDSPDLPK
        0.857
        36780426.667
        62024400.000
        34746250.000
        13570630.000
        10
        tr|A9ERQ5|A9ERQ5_SORC5
        DEREEEDTKR
        0.273
        51547.220
        51547.220
        nan
        nan
        11
        P02769|ALBU_BOVIN
        DLGEEHFK
        0.857
        93178801.333
        157617610.000
        88305880.000
        33612914.000
        12
        P02769|ALBU_BOVIN
        EAC(Carbamidomethyl)FAVEGPK
        0.857
        21342610.000
        31740200.000
        nan
        10945020.000
        13
        P02769|ALBU_BOVIN
        EC(Carbamidomethyl)C(Carbamidomethyl)DKPLLEK
        0.857
        9945544.167
        13641264.000
        13077359.000
        3118009.500
        14
        tr|A9FBB1|A9FBB1_SORC5;tr|A9FBB8|A9FBB8_SORC5
        ELFYDANGNHK
        0.273
        54621.060
        54621.060
        nan
        nan
        15
        P02769|ALBU_BOVIN
        ETYGDM(Oxidation)ADC(Carbamidomethyl)C(Carbamidomethyl)EK
        0.857
        133550.500
        nan
        nan
        133550.500
        16
        P02769|ALBU_BOVIN
        ETYGDMADC(Carbamidomethyl)C(Carbamidomethyl)EK
        0.857
        881499.667
        1547789.000
        688417.300
        408292.700
        17
        P02769|ALBU_BOVIN
        EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK
        0.857
        1222887.500
        1751033.000
        1376247.000
        541382.500
        18
        tr|A9GEZ4|A9GEZ4_SORC5
        EYWM(Oxidation)RLGSIHER
        0.273
        188035.600
        nan
        188035.600
        nan
        19
        tr|A9FJQ1|A9FJQ1_SORC5
        FDKGAR
        0.273
        1821808.000
        1821808.000
        nan
        nan
        20
        sp|O46375|TTHY_BOVIN
        FVEGLYK
        0.857
        3961213.667
        5335508.000
        3643801.000
        2904332.000
        21
        P02769|ALBU_BOVIN
        GAC(Carbamidomethyl)LLPK
        0.857
        6240170.000
        nan
        nan
        6240170.000
        22
        sp|O46375|TTHY_BOVIN
        GSPAANVGVK
        0.857
        790535.100
        790535.100
        nan
        nan
        23
        P02769|ALBU_BOVIN
        HLVDEPQNLIK
        0.857
        87823203.267
        1293139.800
        158439970.000
        103736500.000
        24
        tr|A9FDH1|A9FDH1_SORC5
        ILDFGVSK
        0.273
        92174.850
        nan
        92174.850
        nan
        25
        tr|A9GCG3|A9GCG3_SORC5
        KENSAPK
        0.273
        965206.600
        nan
        nan
        965206.600
        26
        P02769|ALBU_BOVIN
        KQTALVELLK
        0.857
        96691570.000
        nan
        96691570.000
        nan
        27
        P02769|ALBU_BOVIN
        KVPQVSTPTLVEVSR
        0.857
        40396125.000
        nan
        62204730.000
        18587520.000
        28
        O76013|KRT36_HUMAN;O76014|KRT37_HUMAN;O76015|KRT38_HUMAN;Q14525|KT33B_HUMAN;Q14532|K1H2_HUMAN;Q15323|K1H1_HUMAN;Q92764|KRT35_HUMAN
        LAADDFR
        0.556
        42641.250
        nan
        42641.250
        nan
        29
        P02769|ALBU_BOVIN
        LC(Carbamidomethyl)VLHEK
        0.857
        12569310.500
        17642553.000
        17683925.000
        2381453.500
        30
        P62739|ACTA_BOVIN
        LDLAGR
        0.500
        94932.220
        94932.220
        nan
        nan
        31
        P02769|ALBU_BOVIN
        LKPDPNTLC(Carbamidomethyl)DEFK
        0.857
        7899354.000
        nan
        7899354.000
        nan
        32
        P46406|G3P_RABIT
        LTGM(Oxidation)AFR
        0.857
        219603.000
        nan
        219603.000
        nan
        33
        P46406|G3P_RABIT
        LTGMAFR
        0.857
        104067.000
        nan
        104067.000
        nan
        34
        P02769|ALBU_BOVIN
        LVTDLTK
        0.857
        106959906.667
        180142500.000
        89445390.000
        51291830.000
        35
        P02769|ALBU_BOVIN
        LVVSTQTALA
        0.857
        69631885.000
        77023220.000
        62240550.000
        nan
        36
        tr|A9F0I2|A9F0I2_SORC5
        MLKSDVK
        0.273
        950812.500
        nan
        950812.500
        nan
        37
        tr|A9GMF9|A9GMF9_SORC5
        MSDSESDSRR
        0.273
        590296.300
        nan
        590296.300
        nan
        38
        tr|A9FKB2|A9FKB2_SORC5
        MWHHAPM(Oxidation)R
        0.750
        336952.900
        nan
        nan
        336952.900
        39
        tr|A9GKZ3|A9GKZ3_SORC5
        NMRPSK
        0.857
        34508.920
        nan
        34508.920
        nan
        40
        P02769|ALBU_BOVIN
        QEPERNEC(Carbamidomethyl)FLSHK
        0.857
        2348920.750
        163047.500
        4534794.000
        nan
        41
        P02769|ALBU_BOVIN
        QEPERNEC(Carbamidomethyl)FLSHKDDSPDLPK
        0.857
        867965.000
        nan
        867965.000
        nan
        42
        P02769|ALBU_BOVIN
        RHPEYAVSVLLR
        0.857
        13274550.000
        nan
        13274550.000
        nan
        43
        P02769|ALBU_BOVIN
        RPC(Carbamidomethyl)FSALTPDETYVPK
        0.857
        5109413.000
        nan
        5109413.000
        nan
        44
        P02769|ALBU_BOVIN
        SHC(Carbamidomethyl)IAEVEK
        0.857
        909998.600
        1358151.000
        nan
        461846.200
        45
        tr|A9GE86|A9GE86_SORC5
        TWNFDPVGLR
        0.174
        749862.300
        749862.300
        nan
        nan
        46
        P02769|ALBU_BOVIN
        VASLRETYGDM(Oxidation)ADC(Carbamidomethyl)C(Carbamidomethyl)EK
        0.857
        172439.200
        nan
        172439.200
        nan
        47
        P00761|TRYP_PIG
        VATVSLPR
        0.857
        20565010.000
        20565010.000
        nan
        nan
        48
        sp|O46375|TTHY_BOVIN
        VLDAVR
        0.857
        1252257.500
        1605236.000
        899279.000
        nan
        49
        P02769|ALBU_BOVIN
        VPQVSTPTLVEVSR
        0.857
        4498269.050
        nan
        8200278.000
        796260.100
        50
        tr|A9FS16|A9FS16_SORC5
        VRGLGEHLR
        0.273
        579403.000
        579403.000
        nan
        nan
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        Showing 20/20 rows and 8/8 columns.
        ProteinNamePeptides_NumberAverage Intensity123123
        O76013|KRT36_HUMAN;O76014|KRT37_HUMAN;O76015|KRT38_HUMAN;Q14525|KT33B_HUMAN;Q14532|K1H2_HUMAN;Q15323|K1H1_HUMAN;Q92764|KRT35_HUMAN
        1
        42641.250
        nan
        42641.250
        nan
        P00761|TRYP_PIG
        1
        20565010.000
        20565010.000
        nan
        nan
        P02769|ALBU_BOVIN
        28
        779515184.233
        1035079915.300
        912905165.400
        390560472.000
        P46406|G3P_RABIT
        2
        323670.000
        nan
        323670.000
        nan
        P62739|ACTA_BOVIN
        2
        192440.360
        192440.360
        nan
        nan
        sp|O46375|TTHY_BOVIN
        5
        5381326.200
        8501776.700
        4737869.900
        2904332.000
        tr|A9ERQ5|A9ERQ5_SORC5
        1
        51547.220
        51547.220
        nan
        nan
        tr|A9F0I2|A9F0I2_SORC5
        1
        950812.500
        nan
        950812.500
        nan
        tr|A9FBB1|A9FBB1_SORC5;tr|A9FBB8|A9FBB8_SORC5
        1
        54621.060
        54621.060
        nan
        nan
        tr|A9FDH1|A9FDH1_SORC5
        1
        92174.850
        nan
        92174.850
        nan
        tr|A9FJQ1|A9FJQ1_SORC5
        1
        1821808.000
        1821808.000
        nan
        nan
        tr|A9FKB2|A9FKB2_SORC5
        1
        336952.900
        nan
        nan
        336952.900
        tr|A9FP67|A9FP67_SORC5
        1
        355427.600
        355427.600
        nan
        nan
        tr|A9FS16|A9FS16_SORC5
        1
        579403.000
        579403.000
        nan
        nan
        tr|A9GCG3|A9GCG3_SORC5
        1
        965206.600
        nan
        nan
        965206.600
        tr|A9GE86|A9GE86_SORC5
        1
        749862.300
        749862.300
        nan
        nan
        tr|A9GEZ4|A9GEZ4_SORC5
        1
        188035.600
        nan
        188035.600
        nan
        tr|A9GHP5|A9GHP5_SORC5
        1
        16564.080
        nan
        16564.080
        nan
        tr|A9GKZ3|A9GKZ3_SORC5
        1
        34508.920
        nan
        34508.920
        nan
        tr|A9GMF9|A9GMF9_SORC5
        1
        590296.300
        nan
        590296.300
        nan
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        FDRIDPEP FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDPEP IDPosteriorErrorProbability 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDSCORESWITCHER IDScoreSwitcher 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MZMLINDEXING FileConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PROTEOMICSLFQ ProteomicsLFQ 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        hungry_linnaeus
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_lfq,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/lfq_testdata/BSA_design_urls1.tsv
        outdir
        ./results_lfq

        Protein database

        database
        /home/chengxin/lfq_testdata/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta
        decoy_string
        rev

        Database search

        search_engines
        msgf
        instrument
        N/A

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        posterior_probabilities
        fit_distributions
        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein inference

        protein_level_fdr_cutoff
        1.0
        psm_level_fdr_cutoff
        1.0

        Protein Quantification (DDA)

        labelling_type
        label free sample
        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        contrasts
        pairwise
        add_triqler_output
        true

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DDA LFQ
        config_profile_description
        Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A